[Bioperl-l] [Bioperl-guts-l] [14455] bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm: fixed up the gene glyph so that it works properly with CDS-only genes

Jason Stajich jason at bioperl.org
Wed Jan 23 03:14:06 EST 2008


Lincoln -- Thank you, Thank you for this fix!  This takes care of  
inconsistency problems I was having with GFF3 and GFF2 data.  It  
works so much more beautifully now!

-jason
On Jan 22, 2008, at 12:48 PM, Lincoln Stein wrote:

> Revision: 14455
> Author:   lstein
> Date:     2008-01-22 15:48:42 -0500 (Tue, 22 Jan 2008)
>
> Log Message:
> -----------
> fixed up the gene glyph so that it works properly with CDS-only genes
>
> Modified Paths:
> --------------
>     bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm
>
> Modified: bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm
> ===================================================================
> --- bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm	2008-01-22  
> 00:16:02 UTC (rev 14454)
> +++ bioperl-live/trunk/Bio/Graphics/Glyph/gene.pm	2008-01-22  
> 20:48:42 UTC (rev 14455)
> @@ -44,7 +44,9 @@
>
>  sub bump {
>    my $self = shift;
> -  return 1 if $self->{level} == 0; # top level bumps, other levels  
> don't unless specified in config
> +  return 1
> +    if $self->{level} == 0
> +      && lc $self->feature->primary_tag eq 'gene'; # top level  
> bumps, other levels don't unless specified in config
>    return $self->SUPER::bump;
>  }
>
> @@ -92,12 +94,16 @@
>  sub _subfeat {
>    my $class   = shift;
>    my $feature = shift;
> -  if ($feature->primary_tag eq 'gene') {
> +  if (lc $feature->primary_tag eq 'gene') {
>      my @transcripts;
>      for my $t (qw/mRNA tRNA snRNA snoRNA miRNA ncRNA pseudogene/) {
>        push @transcripts, $feature->get_SeqFeatures($t);
>      }
>      return @transcripts;
> +  } elsif (lc $feature->primary_tag eq 'cds') {
> +    my @parts = $feature->get_SeqFeatures();
> +    return ($feature) if $class->{level} == 0 and !@parts;
> +    return @parts;
>    }
>
>    my @subparts;
>
>
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